Activity for Jmol
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Bob Hanson committed [r22664] on Code
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Jmol released /Jmol/Version 16.3/Jmol 16.3.17/Jmol-16.3.17-full.tar.gz
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___Jmol.JmolVersion="16.3.17" // (legacy) also 16.3.18 (swingJS)
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JmolVersion="16.3.17" // (legacy) also 16.3.18 (swingJS)
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Jmol.___JmolVersion="16.3.15" // (legacy) also 16.3.16 (swingJS)
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Jmol.___JmolVersion="16.3.15" // (legacy) also 16.3.16 (swingJS)
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Jmol.___JmolVersion="16.3.13" // (legacy) also 16.3.14 (swingJS)
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Jmol.___JmolVersion="16.3.11" (legacy) // also 16.3.12 (swingJS)
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Jmol.___JmolVersion="16.3.9" // (legacy) also 16.3.10 (SwingJS)
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Angel, nice demo. I think your schema ranges are a bit off. I see here; https://github.com/sokrypton/ColabFold set_color n0, [0.051, 0.341, 0.827] set_color n1, [0.416, 0.796, 0.945] set_color n2, [0.996, 0.851, 0.212] set_color n3, [0.992, 0.490, 0.302] color n0, b < 100; color n1, b < 90 color n2, b < 70; color n3, b < 50 Whereas you are using select (temperature<=0.5); color [xFF7E45]; select (temperature>0.5); color [xFFDB12]; select (temperature>0.7); color [x57CAF9]; select (temperature>0.9);...
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Angel Herraez posted a comment on ticket #266
Thanks. I do not quite get the same result. Similar, but not exactly the same, I guess at threshold values. See test/demo https://biomodel.uah.es/Jmol/fold_AI/test-colors.htm Top row: using conditionals for coloring. Bottom row; using userColorScheme or custom color scheme. Using 10 color values. The file came from ESMfold and has B-values from 0 to 1.
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Sounds good. B factors are normalized internally to 0 to 100 anyway. You can set any discrete set of colors to any set of ranges. You can do this with set usercolorscheme. You would duplicate colors along a range of 0 to 100 stepping every 10. So red red red blue blue blue etc according to your four ranges there. Experiment a bit. If you set that up the way you want it, I can internalize it as a named color scheme.
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new color scheme using pLDDT from prediction servers
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Symmetry, CIFWriter, CLEG, sgmap
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MW Extension
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MW Extension
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MW Extension
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MW Extension
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Good morning, Bob After all the email exchanges between Miguel and Jaime, I did not fully understand what the problem was and why it could not be solved, but... * Miguel is the owner of the jmol.org domain (and would pay for the SSL certificate) * The content is in fact in an Amazon Web Server managed by Jaime (so I assume that Weizmann pays for the hosting, or it is within a larger hoting plan). The subdomain wiki.jmol.org is redirected there. * They say that when the certificate is about to expire,...
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Ok so expired certificate. Next step, On Fri, Jan 17, 2025, 1:56 PM Angel Herraez aherraez@users.sourceforge.net wrote: --- v4 +++ v5 @@ -12,7 +12,21 @@ Using the Extension -... +Several tags will make use of the Extension to insert JSmol objects in different ways, and to interact with them via UI controls like buttons, links.... + +##### Simple tags: +render a link in the page that, when clicked by the user, will open a small window (pop-up) with a JSmol panel that displays a structure. No custom...
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MW Extension
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MW Extension
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Home
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minimal set of JSmol files
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MW Extension
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MW Extension
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MW Extension
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brief description and instructions to accompany the MediaWiki Extension files
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starting version 6 of the Jmol MW Extension (for MW 1.39+)
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starting version 6 of the Jmol MW Extension (for MW 1.39+)
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various fixes Jmol 16.3.8 and 16.3.10(pre)
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splash image - update (c) to 2025
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Jmol.___JmolVersion="16.3.5" // (legacy) also 16.3.6 (SwingJS)
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Jmol.___JmolVersion="16.3.5" // (legacy) also 16.3.6 (SwingJS)
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Jmol.___JmolVersion="16.3.5" // (legacy) also 16.3.6 (SwingJS)
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Jmol 16.3 code
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